vsScatterPlot: Scatter plot of log_{10}(FPKM or CPM) values
In btmonier/ggviseq: Create rapid visualizations of RNAseq data in R

Description Usage Arguments Value Author(s) Examples

This function allows you to visualize comparisons of log_{10} values of either FPKM or CPM measurements of two treatments depending on analytical type.

vsScatterPlot(x, y, data, d.factor = NULL, type = c("cuffdiff", "deseq",
  "edger"), title = TRUE, grid = TRUE, highlight = NULL,
  data.return = FALSE, xaxis.text.size = 10, yaxis.text.size = 10,
  xaxis.title.size = 12, yaxis.title.size = 12, main.title.size = 15)

`x`	treatment `x` for comparison (log_{2}(x/control)). This will be a factor level in your data.
`y`	treatment `y` for comparison (log_{2}(y/control)). This will be a factor level in your data.
`data`	output generated from calling the main routines of either `cuffdiff`, `DESeq2`, or `edgeR` analyses. For `cuffdiff`, this will be a `*_exp.diff` file. For `DESeq2`, this will be a generated object of class `DESeqDataSet`. For `edgeR`, this will be a generated object of class `DGEList`.
`d.factor`	a specified factor; for use with `DESeq2` objects only. This input equates to the first parameter for the contrast argument when invoking the `results()` function in `DESeq2`. Defaults to `NULL`.
`type`	an analysis classifier to tell the function how to process the data. Must be either `cuffdiff`, `deseq`, or `edger`. `cuffdiff` must be used with `cuffdiff` data; `deseq` must be used for `DESeq2` output; `edgeR` must be used with `edgeR` data. See the `data` parameter for further details.
`title`	display the main title of plot. Logical; defaults to `TRUE`. If set to `FALSE`, no title will display in plot.
`grid`	display major and minor axis lines. Logical; defaults to `TRUE`. If set to `FALSE`, no axis lines will display in plot.
`highlight`	character string of IDs that will be highlighted. Set to `NULL` if you do not want highlighted data.
`data.return`	returns data output of plot Logical; defaults to `FALSE`. If set to `TRUE`, a data frame will also be called. Assign to object for reproduction and saving of data frame. See final example for further details.
`xaxis.text.size`	change the font size of the `x`-axis text. Defaults to `10`.
`yaxis.text.size`	change the font size of the `y`-axis text. Defaults to `10`.
`xaxis.title.size`	change the font size of the `x`-axis title text. Defaults to `12`.
`yaxis.title.size`	change the font size of the `y`-axis title text. Defaults to `12`.
`main.title.size`	change the font size of the plot title text. Defaults to `15`.

An object created by ggplot

Brandon Monier, brandon.monier@sdstate.edu

# Cuffdiff example
data("df.cuff")
vsScatterPlot(
     x = "hESC", y = "iPS", data = df.cuff, d.factor = NULL,
     type = "cuffdiff", title = TRUE, grid = TRUE
)

# DESeq2 example
data("df.deseq")
require(DESeq2)
vsScatterPlot(
     x = "treated_paired.end", y = "untreated_paired.end",
     data = df.deseq, d.factor = "condition", type = "deseq",
     title = TRUE, grid = TRUE
)

# edgeR example
data("df.edger")
require(edgeR)
vsScatterPlot(
     x = "WW", y = "WM", data = df.edger, d.factor = NULL,
     type = "edger", title = TRUE, grid = TRUE
)

# Highlight IDs
data("df.cuff")
hl <- c(
     "XLOC_000033",
     "XLOC_000099",
     "XLOC_001414",
     "XLOC_001409"
)
vsScatterPlot(
     x = "hESC", y = "iPS", data = df.cuff, d.factor = NULL,
     type = "cuffdiff", title = TRUE, grid = TRUE, highlight = hl
)

# Extract data frame from visualization
data("df.cuff")
tmp <- vsScatterPlot(
     x = "hESC", y = "iPS", data = df.cuff, d.factor = NULL,
     type = "cuffdiff", title = TRUE, grid = TRUE, data.return = TRUE
)
df_scatter <- tmp[[1]] ## or use tmp$data
head(df_scatter)

# Show plot from object (see prior example for more details)
tmp[[2]] ## or use tmp$plot